[phenixbb] Unexpected Occupancy refiniement for ligands...
Pavel Afonine
pafonine at lbl.gov
Sat Aug 13 10:38:35 PDT 2011
Hi Yuri,
yes, Ed is perfectly right - you don't want to refine occupancies of
water at this resolution (1.5A).
Regarding the ligand: just make sure the occupancies of ligand atoms are
all equal to each other and less than 1 (say 0.9) in your input PDB
file. The rest will be taken care of automatically.
Pavel.
On 8/13/11 8:30 AM, Yuri wrote:
> Hey,
> So I am finishing up a model at 1.5 A and I tried to refine my ligands
> (3) and waters (468) in addition to altloc residues.
> The residues refine as expected e.g OccA + OccB = 1.0 and all atoms in
> A have OccA and all the atoms in B have OccB.
> My ligands on the other are being refined as the following:
>
> HETATM 6867 C1 MLA L 3 32.357 -28.612 7.978 0.93
> 23.77 C C
>
> HETATM 6868 O1A MLA L 3 31.209 -28.949 7.502 0.85
> 24.79 C O
>
> HETATM 6869 O1B MLA L 3 32.454 -28.160 9.141 0.70
> 22.70 C O
>
> HETATM 6870 C2 MLA L 3 33.553 -28.727 7.095 1.00
> 25.46 C C
>
> HETATM 6871 C3 MLA L 3 34.774 -28.070 7.627 0.92
> 28.45 C C
>
> HETATM 6872 O3A MLA L 3 34.830 -27.664 8.808 1.00
> 30.15 C O
>
> HETATM 6873 O3B MLA L 3 35.775 -27.948 6.840 1.00
> 30.23 C O
>
> HETATM 6874 HC21 MLA L 3 33.321 -28.281 6.139 1.00
> 30.56 C H
>
> HETATM 6875 HC22 MLA L 3 33.760 -29.776 6.943 1.00
> 30.56 C H
>
> Each atom is getting an individual occupancy assigned, which
> physically is impossible :)
> Any light?
> Could it be my selection syntax?
>
> Corrigendum: I think I sent a bug email last night about an error when
> writing mtz files in refinement. It was an accident. My naming
> convention was bad, thats why it crashed. Sorry
>
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